Lost atoms: original 42592 current 41916 (src/thermo.cpp:488)

LAMMPS LAMMPS Beginners
1

I’m beginner in lammps. I’ve been trying develop nanoindentation code for Al-Cu-Mg nanorod. My script is here. Why I’ve been facing the issues of lost atoms in every step of indent run zone. Is there any mistake on my code?

3D indenter simulation

units metal
dimension 3
boundary p p p
atom_style atomic

read_data alloy.lmp

pair_style meam
pair_coeff * * library.meam Al Si Mg Cu Fe alloy.meam Al Mg Cu

define groups

region fixed block 0 89.1 0 10 0 89.1
group lower region fixed
region thermo block 0 89.1 10 20 0 89.1
group thermostat region thermo
region mobile block 0 89.1 20 89.1 0 89.1
group mobile region mobile

velocity all create 300.0 12345 mom yes rot no dist gaussian
fix 1 mobile nve
fix 2 thermostat nvt temp 300.0 300.0 0.1
fix 3 lower setforce 0.0 0.0 0.0

------------------ Equilibration Run ------------------

timestep 0.001
thermo 100
fix 4 all npt temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
thermo_style custom step temp press pxx pyy pzz
run 100
unfix 4

run with indenter

reset_timestep 0
variable y equal " 89.1-stepdt0.0001"
print “y is $y”

variable disp equal “stepdt0.0001”
variable f1 equal f_5[1]
variable f2 equal f_5[2]
variable f3 equal f_5[3]
variable load equal “((v_f1)^2 + (v_f2)^2 + (v_f3)^2)^(1/2)”
variable force equal fmax
variable stp equal “step”

Dumps (optional)

fix 5 mobile indent 50 sphere 20 v_y 50 50.0
thermo 100
thermo_style custom step temp v_y f_5[1] f_5[2] f_5[3] fmax #displacement force in all three direction
fix 6 all print 100 “stp{force} ${disp}” title “step load disp” file output_data3.txt screen no
dump 1 all atom 100 dump.indent
run 30000

2
  1. You better read the forum’s rules before dumping your problem without context.
  2. A forum is an archive and it collects useful information. Countless advice has been given to people in your position, so I only take the time to invite you to hit the search button and read what’s already there.
  3. In your script you integrate atoms in the mobile group twice, which leads to bogus results.
3

I’ve corrected it but still facing the same problem. What should I do to fix this problem?

4

Hi @REHAD_SINDID_PATWARY,

This error is common and as @hothello said, there are a lot of ressources on the forum to solve it.

In general, this error appears because of bad configuration, bad model or both. See more details here or as told in the forum other threads.

5

How do we know what you did? I am not the one who should ask you questions to find out what you did, or even if you understood what I said.
Again, you better start by reading the forum rules.

Do you homework: read the LAMMPS script line by line and make sure you understand what the command is doing by reading the documentation. We all did it, there is no shortcut.

6

There are many possible reasons that may lead to atomic loss. It could be that the initial system is problematic, the potential function is inappropriate, or the temperature control is improper. You should check step by step in combination with your instructions.